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Nucleic Acids Research 2004 32(Web Server Issue):W526-W531; doi:10.1093/nar/gkh468
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

Protein structure prediction and analysis using the Robetta server

David E. Kim, Dylan Chivian and David Baker*

Structural Genomics of Pathogenic Protozoa, Department of Biochemistry, University of Washington, Seattle WA 98195, USA

* To whom correspondence should be addressed. Tel: +1 206 543 1295; Fax: +1 206 685 1792; Email: dabaker{at}u.washington.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received February 14, 2004; Revised and Accepted April 29, 2004

The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods. If a confident match to a protein of known structure is found using BLAST, PSI-BLAST, FFAS03 or 3D-Jury, it is used as a template for comparative modeling. If no match is found, structure predictions are made using the de novo Rosetta fragment insertion method. Experimental nuclear magnetic resonance (NMR) constraints data can also be submitted with a query sequence for RosettaNMR de novo structure determination. Other current capabilities include the prediction of the effects of mutations on protein–protein interactions using computational interface alanine scanning. The Rosetta protein design and protein–protein docking methodologies will soon be available through the server as well.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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